USERS
DEVELOPERS


see also:
PROTEGE WIKI
 published papers and technical reports

List of all SMI (and some KSL) Publications
SMI-2005-1080
M. J. O'Connor, H. Knublauch, S. W. Tu, B. Grossof, M. Dean, W. E. Grosso, M. A. Musen. Supporting Rule System Interoperability on the Semantic Web with SWRL. Fourth International Semantic Web Conference (ISWC2005), Galway, Ireland, 2005.
SMI-2005-1079
M. J. O'Connor, H. Knublauch, S. W. Tu, & M. A. Musen. Writing Rules for the Semantic Web Using SWRL and Jess. 8th International Protege Conference, Protege with Rules Workshop, Madrid, Spain, 2005.
SMI-2005-1072
M. Crubezy, M. J. O'Connor, D. L. Buckeridge, Z. S. Pincus, & M. A. Musen. Ontology-Centered Syndromic Surveillance for Bioterrorism. IEEE Intelligent Systems,20(5):26-35. 2005.
SMI-2004-1071
O. Dameron. JOT: a scripting environment for creating and managing ontologies. 7th International Protégé Conference, Bethesda, MD (USA), 2004.
SMI-2004-1070
O. Dameron, N. F. Noy, H. Knublauch, & M. A. Musen. Accessing and manipulating ontologies using web services.. Third International Semantic Web Conference (ISWC2004), Hiroshima, Japan, 2004.
SMI-2004-1069
O. Dameron, B. Gibaud, & M. A. Musen. Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy. First International Workshop on Formal Biomedical Knowledge Representation KRMED04, Whistler, Canada, 2004.
SMI-2005-1068
O. Dameron. Keeping modular and platform-independent software up-to-date: benefits from the Semantic Web. 8th International Protege conference, Madrid, Spain, 2005.
SMI-2005-1067
O. Dameron, D. L. Rubin, & M. A. Musen. Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. AMIA, Washington DC, 2005.
SMI-2004-1013
A. L. Rector, N. Drummond, M. Horridge, J. Rogers, H. Knublauch, R. Stevens, H. Wang, & C. Wroe. OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns. 14th International Conference on Knowledge Engineering and Knowledge Management (EKAW), Whittlebury Hall, UK, 2004.
SMI-2004-1012
H. Knublauch. Ontology-Driven Software Development in the Context of the Semantic Web: An Example Scenario with Protégé/OWL. International Workshop on the Model-Driven Semantic Web, Monterey, CA, 2004.
SMI-2004-1011
H. Knublauch, R. W. Fergerson, N. F. Noy, & M. A. Musen. The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. Third International Semantic Web Conference, Hiroshima, Japan, 2004.
SMI-2004-1007
H. Knublauch, M. A. Musen, & A. L. Rector. Editing Description Logic Ontologies with the Protégé OWL Plugin. International Workshop on Description Logics (DL2004), Whistler, Canada, 2004.
SMI-2004-1006
H. Knublauch, O. Dameron, & M. A. Musen. Weaving the Biomedical Semantic Web with the Protégé OWL Plugin. First International Workshop on Formal Biomedical Knowledge Representation, Whistler, Canada, 2004.
SMI-2003-0989
I. Yeh, P. D. Karp, N. F. Noy, & R. B. Altman. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics,2(January 22):241-8. 2003.
SMI-2003-0973
N. F. Noy & M. A. Musen. The PROMPT Suite: Interactive Tools For Ontology Merging And Mapping. International Journal of Human-Computer Studies,2003.
SMI-2003-0961
N. F. Noy & M. A. Musen. Ontology Versioning as an Element of an Ontology-Evolution Framework. IEEE Intelligent Systems,2003.
SMI-2002-0944
R. D. Shankar, S. W. Tu, & M. A. Musen. Use of Protégé-2000 to Encode Clinical Guidelines. 2002.
SMI-2002-0943
J. Gennari, M. A. Musen, R. W. Fergerson, W. E. Grosso, M. Crubezy, H. Eriksson, N. F. Noy, & S. W. Tu. The Evolution of Protégé: An Environment for Knowledge-Based Systems Development. 2002.
SMI-2002-0936
N. F. Noy, M. A. Musen. Evaluating Ontology-Mapping Tools: Requirements and Experience. 2002.
SMI-2002-0925
N. F. Noy, M. A. Musen, J. L. Mejino, & C. Rosse. Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy. 2002.
SMI-2001-0894
A. T. Schreiber, M. Crubezy, & M. A. Musen. A Case Study in Using Protege-2000 as a Tool for CommonKADS. 12th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France, 2001.
SMI-2001-0889
N. F. Noy & M. A. Musen. Anchor-PROMPT: Using Non-Local Context for Semantic Matching. Workshop on Ontologies and Information Sharing at the Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-2001), Seattle, WA, 2001.
SMI-2001-0880
N. F. Noy & D. L. McGuinness. Ontology Development 101: A Guide to Creating Your First Ontology. 2001.
SMI-2001-0872
N. F. Noy, M. Sintek, S. Decker, M. Crubezy, R. W. Fergerson, & M. A. Musen. Creating Semantic Web Contents with Protege-2000. IEEE Intelligent Systems 16(2):60-71, 2001.
SMI-2000-0850
Q. Li, P. Shilane, N. F. Noy, & M. A. Musen. Ontology Acquisition from On-line Knowledge Sources. AMIA Annual Symposium, Los Angeles, CA, . 2000. 
SMI-2000-0838
M. A. Musen, R. W. Fergerson, W. E. Grosso, N. F. Noy, M. Crubezy, & J. H. Gennari. Component-Based Support for Building Knowledge-Acquisition Systems. Conference on Intelligent Information Processing (IIP 2000) of the International Federation for Information Processing World Computer Congress (WCC 2000), Beijing, . 2000.
SMI-2000-0831
N. F. Noy & M. A. Musen. PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment. Seventeenth National Conference on Artificial Intelligence (AAAI-2000), Austin, TX, . 2000.
SMI-2000-0830
N. F. Noy, R. W. Fergerson, & M. A. Musen. The knowledge model of Protege-2000: Combining interoperability and flexibility. 2th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France, . 2000.
SMI-2000-0825
N. F. Noy, W. Grosso, & M. A. Musen. Knowledge-Acquisition Interfaces for Domain Experts: An Empirical Evaluation of Protege-2000. Twelfth International Conference on Software Engineering and Knowledge Engineering (SEKE2000), Chicago, IL, . 2000.
SMI-1999-0809
H. Eriksson, R. W. Fergerson, Y. Shahar, & M. A. Musen. Automatic Generation of Ontology Editors. Twelfth Banff Knowledge Acquisition for Knowledge-based systems Workshop, Banff, Alberta, Canada, . 1999.
SMI-1999-0808
Y. Shahar & M. Musen. Evaluation of a Temporal-Abstraction Knowledge-Acquisition Tool. Twelfth Banff Knowledge Acquisition for Knowledge-Based Systems Workshop, Banff, Alberta, Canada, . 1999.
SMI-1999-0801
W. E. Grosso, H. Eriksson, R. W. Fergerson, J. H. Gennari, S. W. Tu, & M. A. Musen. Knowledge Modeling at the Millennium (The Design and Evolution of Protege-2000). 1999.
SMI-1999-0799
N. F. Noy & M. A. Musen. An Algorithm for Merging and Aligning Ontologies: Automation and Tool Support. Sixteenth National Conference on Artificial Intelligence (AAAI-99), Workshop on Ontology Management, Orlando, FL, . 1999.
SMI-1999-0789
S. W. Tu & M. A. Musen. A Flexible Approach to Guideline Modeling. 1999.
SMI-1999-0779
D. L. Rubin, J. H. Gennari, S. Srinivas, A. Yuen, H. Kaizer, M. A. Musen, & J. S. Silva. Tool Support for Authoring Eligibility Criteria for Cancer Trials. 1999.
SMI-98-0756
J. Y. Park & M. A. Musen. VM-in-Protege: A Study of Software Reuse. In A.T. McCray B. Cesnik and J.-R. Scherrer, Ed., Medinfo '98: Ninth World Congress on Medical Informatics, Seoul, South Korea, 644-648. IOS Press, 1998.
SMI-98-0734
M. A. Musen. Modern Architectures for Intelligent Systems: Reusable Ontologies and Problem-Solving Methods. In C.G. Chute, Ed., 1998 AMIA Annual Symposium, Orlando, FL, 46-52. 1998.
SMI-98-0733
S. Smith, J. Y. Park, & M. A. Musen. Therapy Planning as Constraint Satisfaction: A Computer-Based Antiretroviral Therapy Advisor for the Management of HIV. In C.G. Chute, Ed., 1998 AMIA Annual Symposium, Orlando, FL, 627-631. 1998.
SMI-97-0697
J. Y. Park, J. H. Gennari, & M. A. Musen. Mappings for Reuse in Knowledge-based Systems. 1997.
SMI-97-0696
W. Grosso, J. Gennari, R. Fergerson, & M. Musen. When Knowledge Models Collide (How it Happens and What to Do). 1997.
SMI-97-0695
J. H. Gennari, W. Grosso, & M. Musen. A Method-Description Language: An initial ontology with examples. 1997.
SMI-97-0687
J. H. Gennari, H. Cheng, R. B. Altman, & M. A. Musen. Reuse, CORBA, and Knowledge-Based Systems. International Journal of Human-Computer Studies 49(4):523-546, 1998.
SMI-97-0681
A. Advani, S. Tu, & M. Musen. Domain Modeling for Integrated Ontologies: Principles for Reconciliation and Reuse. 1997.
SMI-97-0657
M. A. Musen. Domain Ontologies in Software Engineering: Use of Protege with the EON Architecture. Methods of Information in Medicine 37:540-550, 1998.
SMI-96-0648
R. Studer, H. Eriksson, J. Gennari, S. Tu, D. Fensel, & M. Musen. Ontologies and the Configuration of Problem-solving Methods. In B.R. Gains and M.A. Musen, Ed., 10th Banff Knowledge Acquisition for Knowledge-Based Systems Workshop, Banff, Canada, 11-1 - 11-20. 1996.
SMI-96-0631
M. Molina, Y. Shahar, J. Cuena, & M. Musen. A Structure of Problem-solving Methods for Real-time Decision Support: Modeling Approaches Using PROTEGE-II and KSM. In B.R. Gains and M.A. Musen, Ed., 10th Banff Knowledge Acquisition for Knowledge-Based Systems Workshop, Banff, Canada, 8-1 - 8-20. 1996.
SMI-96-0629
J. H. Gennari, A. R. Stein, & M. A. Musen. Reuse for Knowledge-Based Systems and CORBA Components. In B.R. Gains and M.A. Musen, Ed., 10th Banff Knowledge Acquisition for Knowledge-Based Systems Workshop, Banff, Canada, 46-1 - 46-16. 1996.
SMI-96-0620
P. D. Johnson & M. A. Musen. Development of a guideline authoring tool with PROTEGE-II, based on the DILEMMA Generic Protocol and Guideline Model. 1996.
SMI-96-0606
M. Musen, S. Tu, A. Das, & Y. Shahar. EON: A Component-Based Approach to Automation of Protocol-Directed Therapy. JAMIA 3:367-388, 1996.
SMI-96-0602
D. Fensel, H. Eriksson, M. A. Musen, & R. Studer. Conceptual and Formal Specifications of Problem-Solving Methods. International Journal of Expert Systems 9(4):507-532, 1996.
SMI-95-0574
M. A. Musen, J. H. Gennari, & W. W. Wong. A Rational Reconstruction of INTERNIST-I using PROTEGE-II. Nineteenth Annual Symposium on Computer Applications in Medical Care, New Orleans, LA, 289-293. 1995.
SMI-94-0551
H. Eriksson, A. R. Puerta, J. H. Gennari, T. E. Rothenfluh, S. W. Tu, & M. A. Musen. Custom-Tailored Development Tools for Knowledge-Based Systems. Knowledge Systems Laboratory, Medical Computer Science, January 1994.
SMI-94-0549
J. H. Gennari, R. B. Altman, & M. A. Musen. Reuse with Protege-II: From Elevators to Ribosomes. ACM-SigSoft 1995 Symposium on Software Reusability, Seattle, WA, 72-80. 1995.
SMI-94-0545
M. A. Musen, J. H. Gennari, H. Eriksson, S. W. Tu, & A. R. Puerta. PROTEGE II: Computer Support For Development Of Intelligent Systems From Libraries Of Components. MEDINFO 95, The Eighth World Congress on Medical Informatics, Vancouver, B.C., Canada, 766-770. 1995.
SMI-94-0527
Y. Shahar, A. K. Das, S. W. Tu, F. B. Kraemer, & M. A. Musen. Knowledge-Based Temporal Abstraction for Diabetic Monitoring. Eighteenth Annual Symposium on Computer Applications in Medical Care, Washington, DC, 697-701. 1994.
SMI-94-0520
S. W. Tu, H. Eriksson, J. Gennari, Y. Shahar, & M. A. Musen. Ontology-Based Configuration of Problem-Solving Methods and Generation of Knowledge-Acquisition Tools: Application of PROTEGE-II to Protocol-Based Decision Support. Artificial Intelligence in Medicine, 7(Issue):257-289, 1995.
SMI-94-0512
Y. Shahar, A. K. Das, S. W. Tu, & M. A. Musen. Knowledge-Based Temporal Abstraction in Clinical-Management Tasks. AAAI Spring Symposium on Artificial Intelligence in Medicine, Stanford, CA, 143-147. 1994.
SMI-94-0496
H. Eriksson, A. R. Puerta, & M. A. Musen. Generation of Knowledge-Acquisition Tools from Domain Ontologies. International Journal of Human-Computer Studies 41:425-453, 1994.
SMI-93-0502
T. E. Rothenfluh, J. H. Gennari, H. Eriksson, A. R. Puerta, S. W. Tu, & M. A. Musen. Reusable Ontologies, Knowledge-Acquisition Tools, and Performance Systems: PROTEGE-II Solutions to Sisyphus-2. 8th Banff Knowledge Acquisition for Knowledge-Based Workshop, Banff, Alberta, 43-1 to 43-30. 1994.
SMI-93-0501
A. R. Puerta, R. Neches, H. Eriksson, P. Szekely, P. Luo, & M. A. Musen. Toward Ontology-Based Frameworks for Knowledge-Acquisition Tools. Eighth Banff Knowledge-Based Systems Workshop, Banff, Alberta, Canada, 26-1 to 26-14. 1994.
SMI-93-0497
J. H. Gennari, S. W. Tu, T. E. Rothenfluh, & M. A. Musen. Mapping Domains to Methods in Support of Reuse. International Journal of Human-Computer Studies 41:399-424, 1994.
SMI-93-0491
M. A. Musen, S. W. Tu, H. Eriksson, J. H. Gennari, & A. R. Puerta. PROTEGE-II: An Environment for Reusable Problem-Solving Methods and Domain Ontologies. International Joint Conference on Artificial Intelligence, Chambery, Savoie, France, . 1993.
SMI-93-0478
H. Eriksson & M. A. Musen. Metatools for knowledge acquisition. IEEE Software, (Issue):23-29, 1993.
SMI-93-0468
J. W. Egar & M. A. Musen. Automated Modeling of Medical Decisions. Seventeenth Annual Symposium on Computer Applications in Medical Care, Washington, DC, 424-428. 1993.
SMI-92-0454
A. R. Puerta, H. Eriksson, J. W. Egar, & M. A. Musen. Generation of Knowledge-Acquisition Tools from Reusable Domain Ontologies. November 1992.
SMI-92-0441
H. Eriksson, A. R. Puerta, & M. A. Musen. User-Interface Design Based on Data Models for Application Programs. September 1992.
SMI-92-0437
E. Walther, H. Eriksson, & M. A. Musen. Plug-and-Play: Construction of Task-Specific Expert-System Shells Using Sharable Context Ontologies. AAAI Workshop on Knowledge Representation Aspects of Knowledge Acquisition, San Jose, CA, 191-198. AAAI, 1992.
SMI-92-0434
H. Eriksson, Y. Shahar, S. W. Tu, A. R. Puerta, & M. A. Musen. Task Modeling with Reusable Problem-Solving Methods. Artificial Inteligence 79(2):293-326, 1995.
SMI-92-0428
A. R. Puerta, S. W. Tu, & M. A. Musen. In K.M. Ford & J.M. Bradshaw, Ed., Knowledge Acquisition as a Modeling Activity. 129-152.John Wiley, New York, 1993.
SMI-92-0427
H. Eriksson & M. A. Musen. Conceptual Models for Automatic Generation of Knowledge-Acquisition Tools. Knowledge Engineering Review, 8(Issue):27-47, 1993.
SMI-91-0398
M. A. Musen. Dimensions of Knowledge Sharing and Reuse. Computers and Biomedical Research, 25(Issue):435-467, 1992.
SMI-91-0367
A. Puerta, J. Egar, S. Tu, & M. Musen. A Multiple-Method Knowledge-Acquisition Shell for the Automatic Generation of Knowledge-Acquisition Tools. Sixth Workshop on Knowledge Acquisition for Knowledge-Based Systems, Banff, Alberta, 20-1 to 20-19. 1992.